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Evolutionary principles of modular gene regulation in Yeasts

ABSTRACT: Comparative time-series expression analysis of growth curves through carbon depletion in the ascomycete yeasts

ORGANISM(S): Lachancea waltii Saccharomyces bayanus Saccharomyces cerevisiae Nakaseomyces glabratus Schizosaccharomyces japonicus Saccharomyces mikatae Saccharomyces paradoxus Debaryomyces hansenii Yarrowia lipolytica Schizosaccharomyces pombe Vanderwaltozyma polyspora Lachancea kluyveri NRRL Y-12651 Candida albicans Naumovozyma castellii Lachancea kluyveri Kluyveromyces lactis

PROVIDER: GSE36253 | GEO | 2013/06/20

SECONDARY ACCESSION(S): PRJNA153069

REPOSITORIES: GEO

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Evolutionary principles of modular gene regulation in Yeasts

Project description:Comparative time-series expression analysis of growth curves through carbon depletion in the ascomycete yeasts.

2013-04-25 | GSE38478 | GEO

Evolutionary principles of modular gene regulation in Yeasts

Project description:Comparative time-series expression analysis of growth curves through carbon depletion in the ascomycete yeasts Each of the following species-specific, growth curve derived samples competitively hybed to their own mid-log samples: lag phase, late log, diauxic shift, post-shift, plateau

2013-06-20 | E-GEOD-36253 | biostudies-arrayexpress

Evolutionary principles of modular gene regulation in Yeasts

Project description:Comparative time-series expression analysis of growth curves through carbon depletion in the ascomycete yeasts. Each of the following species-specific, growth curve derived samples competitively hybed to their own mid-log samples: lag phase, late log, diauxic shift, post-shift, plateau.

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Evolutionary principles of modular gene regulation in Yeasts

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Evolutionary principles of modular gene regulation in Yeasts

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Evolutionary principles of modular gene regulation in yeasts.

Project description:Divergence in gene regulation can play a major role in evolution. Here, we used a phylogenetic framework to measure mRNA profiles in 15 yeast species from the phylum Ascomycota and reconstruct the evolution of their modular regulatory programs along a time course of growth on glucose over 300 million years [corrected]. We found that modules have diverged proportionally to phylogenetic distance, with prominent changes in gene regulation accompanying changes in lifestyle and ploidy, especially in carbon metabolism. Paralogs have significantly contributed to regulatory divergence, typically within a very short window from their duplication. Paralogs from a whole genome duplication (WGD) event have a uniquely substantial contribution that extends over a longer span. Similar patterns occur when considering the evolution of the heat shock regulatory program measured in eight of the species, suggesting that these are general evolutionary principles. DOI:http://dx.doi.org/10.7554/eLife.00603.001.

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Project description:Comparative expression analysis of HOG1 KOs during osmotic stress in the ascomycete yeasts

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The evolution, evolvability, and engineering of gene regulatory DNA [RNA-seq]

Project description:Here, we used RNA-seq to quantify expression conservation across many Ascomycete yeasts.

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Project description:Mix of 11 yeasts species metagenome

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Evolutionary Instability of CUG-Leu in the Genetic Code of Budding Yeasts

Project description:The standard genetic code is almost universal, and the evolutionary factors that caused a few organisms to deviate from it are poorly understood. We report that three independent changes of the genetic code occurred during the evolution of budding yeasts, each of which was a reassignment of the codon CUG from leucine to another amino acid. We identify five major yeast clades that differ by translating CUG as either Ser (2 clades), Ala (1 clade), or Leu (2 clades). The newly discovered Ser2 clade is in the final stages of transition from one genetic code to another. It appears to use only a novel tRNASer (tSCAG) to translate CUG codons, but the gene for the ancestral tRNALeu (tLCAG) is still intact in most species in the clade, consistent with the ‘ambiguous intermediate’ theory. We propose that the three parallel changes of the genetic code in yeasts were not driven by natural selection in favor of their effects on the proteome, but by selection to eliminate the ancestral tLCAG, possibly in response to a killer toxin.

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